The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery von Papaleo, Elena, Saladino, Giorgio, Lambrughi, Matteo, Lindorff-Larsen, Kresten, Gervasio, Francesco Luigi, Nussinov, Ruth

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New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx von Mounir, Mohamed, Lucchetta, Marta, Silva, Tiago C, Olsen, Catharina, Bontempi, Gianluca, Chen, Xi, Noushmehr, Houtan, Colaprico, Antonio, Papaleo, Elena

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Excessive aggregation of membrane proteins in the Martini model von Javanainen, Matti, Martinez-Seara, Hector, Vattulainen, Ilpo

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An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations von Nygaard, Mads, Kragelund, Birthe B., Papaleo, Elena, Lindorff-Larsen, Kresten

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Hypothetical Outcome Plots Outperform Error Bars and Violin Plots for Inferences about Reliability of Variable Ordering von Hullman, Jessica, Resnick, Paul, Adar, Eytan

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Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level von Kønig, Simon Mathis, Rissler, Vendela, Terkelsen, Thilde, Lambrughi, Matteo, Papaleo, Elena

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DisProt: intrinsic protein disorder annotation in 2020 von Hatos, András, Hajdu-Soltész, Borbála, Monzon, Alexander M, Palopoli, Nicolas, Álvarez, Lucía, Aykac-Fas, Burcu, Bassot, Claudio, Benítez, Guillermo I, Bevilacqua, Martina, Chasapi, Anastasia, Chemes, Lucia, Davey, Norman E, Davidović, Radoslav, Dunker, A Keith, Elofsson, Arne, Gobeill, Julien, Foutel, Nicolás S González, Sudha, Govindarajan, Guharoy, Mainak, Horvath, Tamas, Iglesias, Valentin, Kajava, Andrey V, Kovacs, Orsolya P, Lamb, John, Lambrughi, Matteo, Lazar, Tamas, Leclercq, Jeremy Y, Leonardi, Emanuela, Macedo-Ribeiro, Sandra, Macossay-Castillo, Mauricio, Maiani, Emiliano, Manso, José A, Marino-Buslje, Cristina, Martínez-Pérez, Elizabeth, Mészáros, Bálint, Mičetić, Ivan, Minervini, Giovanni, Murvai, Nikoletta, Necci, Marco, Ouzounis, Christos A, Pajkos, Mátyás, Paladin, Lisanna, Pancsa, Rita, Papaleo, Elena, Parisi, Gustavo, Pasche, Emilie, Barbosa Pereira, Pedro J, Promponas, Vasilis J, Pujols, Jordi, Quaglia, Federica, Ruch, Patrick, Salvatore, Marco, Schad, Eva, Szabo, Beata, Szaniszló, Tamás, Tamana, Stella, Tantos, Agnes, Veljkovic, Nevena, Ventura, Salvador, Vranken, Wim, Dosztányi, Zsuzsanna, Tompa, Peter, Tosatto, Silvio C E, Piovesan, Damiano

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HUWE1 E3 ligase promotes PINK1/PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKα von Di Rita, Anthea, Peschiaroli, Angelo, D′Acunzo, Pasquale, Strobbe, Daniela, Hu, Zehan, Gruber, Jens, Nygaard, Mads, Lambrughi, Matteo, Melino, Gerry, Papaleo, Elena, Dengjel, Jörn, El Alaoui, Said, Campanella, Michelangelo, Dötsch, Volker, Rogov, Vladimir V., Strappazzon, Flavie, Cecconi, Francesco

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An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass von Salamanca Viloria, Juan, Allega, Maria Francesca, Lambrughi, Matteo, Papaleo, Elena

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DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation von Quaglia, Federica, Mészáros, Bálint, Salladini, Edoardo, Hatos, András, Pancsa, Rita, Chemes, Lucía B, Pajkos, Mátyás, Lazar, Tamas, Peña-Díaz, Samuel, Santos, Jaime, Ács, Veronika, Farahi, Nazanin, Fichó, Erzsébet, Aspromonte, Maria Cristina, Bassot, Claudio, Chasapi, Anastasia, Davey, Norman E, Davidović, Radoslav, Dobson, Laszlo, Elofsson, Arne, Erdős, Gábor, Gaudet, Pascale, Giglio, Michelle, Glavina, Juliana, Iserte, Javier, Iglesias, Valentín, Kálmán, Zsófia, Lambrughi, Matteo, Leonardi, Emanuela, Longhi, Sonia, Macedo-Ribeiro, Sandra, Maiani, Emiliano, Marchetti, Julia, Marino-Buslje, Cristina, Mészáros, Attila, Monzon, Alexander Miguel, Minervini, Giovanni, Nadendla, Suvarna, Nilsson, Juliet F, Novotný, Marian, Ouzounis, Christos A, Palopoli, Nicolás, Papaleo, Elena, Pereira, Pedro José Barbosa, Pozzati, Gabriele, Promponas, Vasilis J, Pujols, Jordi, Rocha, Alma Carolina Sanchez, Salas, Martin, Sawicki, Luciana Rodriguez, Schad, Eva, Shenoy, Aditi, Szaniszló, Tamás, Tsirigos, Konstantinos D, Veljkovic, Nevena, Parisi, Gustavo, Ventura, Salvador, Dosztányi, Zsuzsanna, Tompa, Peter, Tosatto, Silvio C E, Piovesan, Damiano

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Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response von Tee, Wei-Ven, Guarnera, Enrico, Berezovsky, Igor N

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How well do force fields capture the strength of salt bridges in proteins? von Ahmed, Mustapha Carab, Papaleo, Elena, Lindorff-Larsen, Kresten

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Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response von Lucchetta, Marta, da Piedade, Isabelle, Mounir, Mohamed, Vabistsevits, Marina, Terkelsen, Thilde, Papaleo, Elena

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Mapping transiently formed and sparsely populated conformations on a complex energy landscape von Wang, Yong, Papaleo, Elena, Lindorff-Larsen, Kresten

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Interpreting pathways to discover cancer driver genes with Moonlight von Colaprico, Antonio, Olsen, Catharina, Bailey, Matthew H., Odom, Gabriel J., Terkelsen, Thilde, Silva, Tiago C., Olsen, André V., Cantini, Laura, Zinovyev, Andrei, Barillot, Emmanuel, Noushmehr, Houtan, Bertoli, Gloria, Castiglioni, Isabella, Cava, Claudia, Bontempi, Gianluca, Chen, Xi Steven, Papaleo, Elena

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PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins von Tiberti, Matteo, Invernizzi, Gaetano, Lambrughi, Matteo, Inbar, Yuval, Schreiber, Gideon, Papaleo, Elena

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Integrative modeling of diverse protein-peptide systems using CABS-dock von Pulawski, Wojciech, Kolinski, Andrzej, Kolinski, Michal

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Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics von Gueto-Tettay, Carlos, Tang, Di, Happonen, Lotta, Heusel, Moritz, Khakzad, Hamed, Malmström, Johan, Malmström, Lars

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ENCORE: Software for Quantitative Ensemble Comparison von Tiberti, Matteo, Papaleo, Elena, Bengtsen, Tone, Boomsma, Wouter, Lindorff-Larsen, Kresten

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Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration von Terkelsen, Thilde, Russo, Francesco, Gromov, Pavel, Haakensen, Vilde Drageset, Brunak, Soren, Gromova, Irina, Krogh, Anders, Papaleo, Elena

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